Starting phenix.real_space_refine on Fri Jul 3 13:26:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d97_27257/07_2026/8d97_27257.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d97_27257/07_2026/8d97_27257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8d97_27257/07_2026/8d97_27257.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d97_27257/07_2026/8d97_27257.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d97_27257/07_2026/8d97_27257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d97_27257/07_2026/8d97_27257.map" model { file = "/net/cci-nas-00/data/ceres_data/8d97_27257/07_2026/8d97_27257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d97_27257/07_2026/8d97_27257.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.031 sd= 1.128 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 42 5.49 5 S 41 5.16 5 C 8625 2.51 5 N 2445 2.21 5 O 2717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13874 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1600, 12990 Classifications: {'peptide': 1600} Link IDs: {'PTRANS': 70, 'TRANS': 1529} Chain breaks: 8 Chain: "C" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 880 Classifications: {'RNA': 42} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 11, 'rna3p_pur': 5, 'rna3p_pyr': 15} Link IDs: {'rna2p': 21, 'rna3p': 20} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 668 SG CYS A 83 42.188 58.213 17.775 1.00112.54 S ATOM 939 SG CYS A 116 42.722 55.946 14.103 1.00121.93 S ATOM 985 SG CYS A 122 44.991 56.202 17.287 1.00100.15 S ATOM 1009 SG CYS A 125 41.791 54.844 17.275 1.00 97.33 S ATOM 3703 SG CYS A 486 34.125 74.468 46.993 1.00 79.62 S ATOM 3771 SG CYS A 496 35.438 72.708 43.943 1.00 73.06 S ATOM 3785 SG CYS A 498 37.071 75.312 45.520 1.00 71.64 S ATOM 3807 SG CYS A 501 38.009 71.893 46.011 1.00 70.88 S ATOM 5778 SG CYS A 745 25.020 80.291 78.130 1.00140.63 S ATOM 5791 SG CYS A 747 28.461 81.408 78.582 1.00121.80 S ATOM 5813 SG CYS A 750 29.191 78.549 76.694 1.00105.45 S ATOM 7764 SG CYS A1013 31.267 68.320 113.568 1.00118.39 S ATOM 10846 SG CYS A1401 28.623 68.577 111.063 1.00125.65 S ATOM 10897 SG CYS A1409 30.301 71.505 112.762 1.00106.08 S ATOM 10914 SG CYS A1412 32.758 70.068 110.750 1.00102.04 S Time building chain proxies: 2.98, per 1000 atoms: 0.21 Number of scatterers: 13874 At special positions: 0 Unit cell: (88.596, 110.424, 186.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 41 16.00 P 42 15.00 O 2717 8.00 N 2445 7.00 C 8625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1160 " - pdb=" SG CYS A1166 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 660.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 116 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 122 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 83 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 125 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 498 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 486 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 496 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 745 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 747 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1703 " - pdb=" ND1 HIS A 742 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1013 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1401 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1412 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1409 " Number of angles added : 21 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 20 sheets defined 32.6% alpha, 22.5% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 22 through 26 Processing helix chain 'A' and resid 27 through 33 Processing helix chain 'A' and resid 54 through 73 removed outlier: 3.935A pdb=" N VAL A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.645A pdb=" N ILE A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 262 through 282 removed outlier: 3.524A pdb=" N ASP A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 298 removed outlier: 4.216A pdb=" N ARG A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP A 293 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 302 removed outlier: 4.489A pdb=" N GLY A 302 " --> pdb=" O ARG A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 299 through 302' Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.899A pdb=" N GLU A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 Processing helix chain 'A' and resid 349 through 369 Processing helix chain 'A' and resid 466 through 483 removed outlier: 3.559A pdb=" N LEU A 470 " --> pdb=" O PRO A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 505 Processing helix chain 'A' and resid 564 through 575 Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.625A pdb=" N THR A 592 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 620 Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 625 through 632 removed outlier: 3.503A pdb=" N LEU A 629 " --> pdb=" O LYS A 625 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 631 " --> pdb=" O LYS A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 681 through 688 Processing helix chain 'A' and resid 718 through 735 removed outlier: 3.560A pdb=" N PHE A 726 " --> pdb=" O HIS A 722 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 733 " --> pdb=" O ALA A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 775 removed outlier: 3.611A pdb=" N GLU A 774 " --> pdb=" O ASN A 771 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 775 " --> pdb=" O GLY A 772 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 771 through 775' Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.811A pdb=" N LYS A 799 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 843 Processing helix chain 'A' and resid 868 through 877 Processing helix chain 'A' and resid 994 through 1011 removed outlier: 3.944A pdb=" N LEU A 998 " --> pdb=" O PRO A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1039 removed outlier: 3.740A pdb=" N LYS A1037 " --> pdb=" O ALA A1034 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR A1039 " --> pdb=" O GLU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1052 Processing helix chain 'A' and resid 1054 through 1058 removed outlier: 3.651A pdb=" N ARG A1058 " --> pdb=" O PRO A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1069 Processing helix chain 'A' and resid 1083 through 1090 removed outlier: 3.991A pdb=" N SER A1087 " --> pdb=" O ARG A1083 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP A1088 " --> pdb=" O ARG A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1144 through 1148 Processing helix chain 'A' and resid 1152 through 1157 Processing helix chain 'A' and resid 1163 through 1201 removed outlier: 4.015A pdb=" N ARG A1167 " --> pdb=" O SER A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1210 Processing helix chain 'A' and resid 1228 through 1230 No H-bonds generated for 'chain 'A' and resid 1228 through 1230' Processing helix chain 'A' and resid 1327 through 1341 Processing helix chain 'A' and resid 1346 through 1354 Processing helix chain 'A' and resid 1395 through 1399 Processing helix chain 'A' and resid 1409 through 1415 Processing helix chain 'A' and resid 1458 through 1463 removed outlier: 4.457A pdb=" N SER A1462 " --> pdb=" O ARG A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1486 removed outlier: 3.888A pdb=" N ILE A1485 " --> pdb=" O GLY A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1496 removed outlier: 3.515A pdb=" N ARG A1493 " --> pdb=" O GLN A1489 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A1494 " --> pdb=" O LEU A1490 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A1496 " --> pdb=" O ILE A1492 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1535 Processing helix chain 'A' and resid 1581 through 1596 Processing helix chain 'A' and resid 1610 through 1613 removed outlier: 3.757A pdb=" N VAL A1613 " --> pdb=" O GLN A1610 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1610 through 1613' Processing helix chain 'A' and resid 1614 through 1624 Processing helix chain 'A' and resid 1668 through 1678 Processing sheet with id=AA1, first strand: chain 'A' and resid 146 through 148 removed outlier: 3.890A pdb=" N LEU A 153 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER A 51 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 37 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TRP A 190 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N GLU A 17 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 13.243A pdb=" N ARG A 188 " --> pdb=" O GLU A 17 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 183 through 191 current: chain 'A' and resid 230 through 235 Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 176 removed outlier: 6.181A pdb=" N SER A 169 " --> pdb=" O TRP A 190 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TRP A 190 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG A 171 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG A 188 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU A 173 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR A 186 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG A 175 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 13.243A pdb=" N ARG A 188 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N GLU A 17 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TRP A 190 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 37 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER A 51 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 153 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 106 removed outlier: 6.229A pdb=" N THR A 105 " --> pdb=" O VAL A 400 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 507 through 508 removed outlier: 6.673A pdb=" N GLU A 410 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU A 606 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 412 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 604 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 414 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 602 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 507 through 508 removed outlier: 6.673A pdb=" N GLU A 410 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU A 606 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 412 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 604 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 414 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 602 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 521 through 525 Processing sheet with id=AA8, first strand: chain 'A' and resid 698 through 699 removed outlier: 6.234A pdb=" N PHE A 715 " --> pdb=" O LEU A 769 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG A 818 " --> pdb=" O GLU A 765 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A 767 " --> pdb=" O LYS A 816 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LYS A 816 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU A 769 " --> pdb=" O LYS A 814 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LYS A 814 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 703 removed outlier: 3.551A pdb=" N ALA A 708 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 782 through 784 Processing sheet with id=AB2, first strand: chain 'A' and resid 915 through 916 Processing sheet with id=AB3, first strand: chain 'A' and resid 919 through 922 Processing sheet with id=AB4, first strand: chain 'A' and resid 986 through 987 removed outlier: 7.460A pdb=" N LEU A 991 " --> pdb=" O TYR A1431 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A1431 " --> pdb=" O LEU A 991 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A1512 " --> pdb=" O GLU A1432 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU A 945 " --> pdb=" O ASN A1521 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS A 952 " --> pdb=" O ILE A1559 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE A1559 " --> pdb=" O LYS A 952 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU A 954 " --> pdb=" O ILE A1557 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE A1557 " --> pdb=" O GLU A 954 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A1555 " --> pdb=" O HIS A1542 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1424 through 1426 removed outlier: 6.060A pdb=" N LEU A 945 " --> pdb=" O ASN A1521 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS A 952 " --> pdb=" O ILE A1559 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE A1559 " --> pdb=" O LYS A 952 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU A 954 " --> pdb=" O ILE A1557 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE A1557 " --> pdb=" O GLU A 954 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A1564 " --> pdb=" O LYS A1575 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 981 through 982 removed outlier: 7.279A pdb=" N TYR A 982 " --> pdb=" O GLU A1505 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1323 through 1326 removed outlier: 4.546A pdb=" N LEU A1125 " --> pdb=" O VAL A1326 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A1380 " --> pdb=" O HIS A1371 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1131 through 1136 removed outlier: 8.876A pdb=" N VAL A1132 " --> pdb=" O VAL A1232 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ALA A1234 " --> pdb=" O VAL A1132 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG A1134 " --> pdb=" O ALA A1234 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1255 through 1258 Processing sheet with id=AC1, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 3.836A pdb=" N ARG A1292 " --> pdb=" O GLU A1282 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1416 through 1417 497 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3223 1.33 - 1.45: 3177 1.45 - 1.57: 7719 1.57 - 1.69: 83 1.69 - 1.81: 56 Bond restraints: 14258 Sorted by residual: bond pdb=" C ASP A 933 " pdb=" N ILE A 934 " ideal model delta sigma weight residual 1.335 1.317 0.018 1.41e-02 5.03e+03 1.55e+00 bond pdb=" C GLY A1115 " pdb=" O GLY A1115 " ideal model delta sigma weight residual 1.237 1.225 0.012 9.70e-03 1.06e+04 1.44e+00 bond pdb=" C3' G C 45 " pdb=" C2' G C 45 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.50e-02 4.44e+03 1.43e+00 bond pdb=" C4' G C 45 " pdb=" O4' G C 45 " ideal model delta sigma weight residual 1.451 1.434 0.017 1.50e-02 4.44e+03 1.27e+00 bond pdb=" C LYS A 976 " pdb=" O LYS A 976 " ideal model delta sigma weight residual 1.249 1.240 0.009 8.50e-03 1.38e+04 1.06e+00 ... (remaining 14253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 18333 1.31 - 2.61: 905 2.61 - 3.92: 134 3.92 - 5.22: 19 5.22 - 6.53: 6 Bond angle restraints: 19397 Sorted by residual: angle pdb=" C2' G C 45 " pdb=" C1' G C 45 " pdb=" N9 G C 45 " ideal model delta sigma weight residual 112.00 118.53 -6.53 1.50e+00 4.44e-01 1.89e+01 angle pdb=" N GLY A1472 " pdb=" CA GLY A1472 " pdb=" C GLY A1472 " ideal model delta sigma weight residual 110.29 115.52 -5.23 1.28e+00 6.10e-01 1.67e+01 angle pdb=" N LYS A 911 " pdb=" CA LYS A 911 " pdb=" C LYS A 911 " ideal model delta sigma weight residual 114.56 109.74 4.82 1.27e+00 6.20e-01 1.44e+01 angle pdb=" N ASN A1252 " pdb=" CA ASN A1252 " pdb=" C ASN A1252 " ideal model delta sigma weight residual 110.91 115.25 -4.34 1.17e+00 7.31e-01 1.38e+01 angle pdb=" C PRO A1435 " pdb=" N GLU A1436 " pdb=" CA GLU A1436 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 1.00e+01 ... (remaining 19392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 8274 34.82 - 69.64: 217 69.64 - 104.46: 26 104.46 - 139.28: 1 139.28 - 174.10: 3 Dihedral angle restraints: 8521 sinusoidal: 3926 harmonic: 4595 Sorted by residual: dihedral pdb=" C4' G C 26 " pdb=" C3' G C 26 " pdb=" C2' G C 26 " pdb=" C1' G C 26 " ideal model delta sinusoidal sigma weight residual -35.00 31.58 -66.58 1 8.00e+00 1.56e-02 9.04e+01 dihedral pdb=" C5' G C 26 " pdb=" C4' G C 26 " pdb=" C3' G C 26 " pdb=" O3' G C 26 " ideal model delta sinusoidal sigma weight residual 147.00 83.00 64.00 1 8.00e+00 1.56e-02 8.43e+01 dihedral pdb=" O4' C C 22 " pdb=" C1' C C 22 " pdb=" N1 C C 22 " pdb=" C2 C C 22 " ideal model delta sinusoidal sigma weight residual 200.00 55.93 144.07 1 1.50e+01 4.44e-03 7.72e+01 ... (remaining 8518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1764 0.056 - 0.113: 271 0.113 - 0.169: 42 0.169 - 0.226: 1 0.226 - 0.282: 2 Chirality restraints: 2080 Sorted by residual: chirality pdb=" C3' G C 26 " pdb=" C4' G C 26 " pdb=" O3' G C 26 " pdb=" C2' G C 26 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C1' G C 45 " pdb=" O4' G C 45 " pdb=" C2' G C 45 " pdb=" N9 G C 45 " both_signs ideal model delta sigma weight residual False 2.46 2.19 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C2' G C 26 " pdb=" C3' G C 26 " pdb=" O2' G C 26 " pdb=" C1' G C 26 " both_signs ideal model delta sigma weight residual False -2.52 -2.73 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2077 not shown) Planarity restraints: 2367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 45 " 0.047 2.00e-02 2.50e+03 2.11e-02 1.34e+01 pdb=" N9 G C 45 " -0.053 2.00e-02 2.50e+03 pdb=" C8 G C 45 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G C 45 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G C 45 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G C 45 " 0.006 2.00e-02 2.50e+03 pdb=" O6 G C 45 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G C 45 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G C 45 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G C 45 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G C 45 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G C 45 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 957 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO A 958 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 958 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 958 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1684 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO A1685 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1685 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1685 " 0.024 5.00e-02 4.00e+02 ... (remaining 2364 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 303 2.67 - 3.23: 13187 3.23 - 3.79: 20312 3.79 - 4.34: 27173 4.34 - 4.90: 44303 Nonbonded interactions: 105278 Sorted by model distance: nonbonded pdb=" O CYS A 745 " pdb="ZN ZN A1703 " model vdw 2.113 2.230 nonbonded pdb=" NH1 ARG A 723 " pdb=" OP1 A C 32 " model vdw 2.189 3.120 nonbonded pdb=" O GLU A1455 " pdb=" O2' C C 42 " model vdw 2.190 3.040 nonbonded pdb=" O PRO A1668 " pdb=" OG1 THR A1671 " model vdw 2.192 3.040 nonbonded pdb=" O GLN A 904 " pdb=" NZ LYS A1622 " model vdw 2.195 3.120 ... (remaining 105273 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.990 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.609 14275 Z= 0.255 Angle : 0.973 58.763 19420 Z= 0.421 Chirality : 0.043 0.282 2080 Planarity : 0.004 0.044 2367 Dihedral : 16.087 174.102 5572 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.18), residues: 1582 helix: -1.05 (0.21), residues: 453 sheet: -1.35 (0.29), residues: 262 loop : -2.03 (0.19), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 464 TYR 0.014 0.001 TYR A 644 PHE 0.022 0.001 PHE A1085 TRP 0.017 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (14258) covalent geometry : angle 0.64286 / 0.40 (19397) SS BOND : bond 0.00095 / 0.05 ( 1) SS BOND : angle 0.34035 / 0.19 ( 2) hydrogen bonds : bond 0.17093 / 10.49 ( 447) hydrogen bonds : angle 6.34465 / 4.36 ( 1368) metal coordination : bond 0.18743 / 13.78 ( 16) metal coordination : angle 22.23980 / 13.47 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 874 MET cc_start: 0.9169 (mtm) cc_final: 0.8432 (mtp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1266 time to fit residues: 8.8522 Evaluate side-chains 28 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS A 264 HIS A 282 ASN A 323 HIS A 610 ASN A 866 ASN A1033 ASN A1076 ASN A1140 ASN A1207 GLN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 ASN A1487 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.122845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.073027 restraints weight = 37159.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.074920 restraints weight = 19419.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.075925 restraints weight = 13798.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.076420 restraints weight = 11708.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.076770 restraints weight = 10809.408| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 14275 Z= 0.167 Angle : 0.573 13.576 19420 Z= 0.288 Chirality : 0.042 0.161 2080 Planarity : 0.004 0.043 2367 Dihedral : 12.204 170.604 2257 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.92 % Allowed : 8.56 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.20), residues: 1582 helix: 0.25 (0.24), residues: 452 sheet: -1.15 (0.29), residues: 271 loop : -1.49 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 377 TYR 0.012 0.001 TYR A 644 PHE 0.016 0.001 PHE A1353 TRP 0.012 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (14258) covalent geometry : angle 0.54135 / 0.29 (19397) SS BOND : bond 0.00104 / 0.05 ( 1) SS BOND : angle 0.47714 / 0.26 ( 2) hydrogen bonds : bond 0.04345 / 2.78 ( 447) hydrogen bonds : angle 5.04228 / 3.46 ( 1368) metal coordination : bond 0.02579 / 1.92 ( 16) metal coordination : angle 5.71602 / 3.60 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.9243 (tpp) cc_final: 0.8931 (tpp) REVERT: A 583 MET cc_start: 0.8740 (mmm) cc_final: 0.7501 (mmm) REVERT: A 825 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8454 (m-10) REVERT: A 874 MET cc_start: 0.9006 (mtm) cc_final: 0.8321 (mtp) outliers start: 13 outliers final: 3 residues processed: 44 average time/residue: 0.1235 time to fit residues: 8.4831 Evaluate side-chains 33 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1039 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 17 optimal weight: 2.9990 chunk 113 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 131 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 ASN ** A1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.120533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.071066 restraints weight = 37841.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.072842 restraints weight = 20038.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.073842 restraints weight = 14336.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.074331 restraints weight = 12147.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.074711 restraints weight = 11200.263| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 14275 Z= 0.311 Angle : 0.659 12.953 19420 Z= 0.334 Chirality : 0.046 0.191 2080 Planarity : 0.004 0.049 2367 Dihedral : 12.098 174.653 2257 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.27 % Allowed : 11.75 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.20), residues: 1582 helix: 0.57 (0.24), residues: 441 sheet: -1.21 (0.29), residues: 275 loop : -1.41 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 464 TYR 0.011 0.002 TYR A 644 PHE 0.021 0.002 PHE A1353 TRP 0.016 0.002 TRP A1030 HIS 0.007 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.31 (14258) covalent geometry : angle 0.63590 / 0.33 (19397) SS BOND : bond 0.00155 / 0.08 ( 1) SS BOND : angle 0.61835 / 0.34 ( 2) hydrogen bonds : bond 0.04909 / 3.11 ( 447) hydrogen bonds : angle 5.22219 / 3.59 ( 1368) metal coordination : bond 0.01939 / 1.00 ( 16) metal coordination : angle 5.34328 / 3.25 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 32 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.9336 (tpp) cc_final: 0.8992 (tpp) REVERT: A 825 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8618 (m-10) REVERT: A 874 MET cc_start: 0.9123 (mtm) cc_final: 0.8462 (mtp) REVERT: A 1436 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8404 (tm-30) REVERT: A 1458 ARG cc_start: 0.7871 (mmt180) cc_final: 0.6946 (mmm-85) REVERT: A 1507 MET cc_start: 0.8533 (mmm) cc_final: 0.8301 (mmm) outliers start: 18 outliers final: 9 residues processed: 48 average time/residue: 0.0929 time to fit residues: 7.0284 Evaluate side-chains 39 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 913 LYS Chi-restraints excluded: chain A residue 951 CYS Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1436 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 117 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.123032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.073489 restraints weight = 37432.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.075342 restraints weight = 19221.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.076482 restraints weight = 13696.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.076977 restraints weight = 11413.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.077325 restraints weight = 10511.614| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14275 Z= 0.142 Angle : 0.518 10.835 19420 Z= 0.266 Chirality : 0.041 0.157 2080 Planarity : 0.004 0.048 2367 Dihedral : 11.851 173.695 2257 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.78 % Allowed : 13.73 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.21), residues: 1582 helix: 0.91 (0.25), residues: 449 sheet: -1.03 (0.30), residues: 275 loop : -1.22 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 467 TYR 0.011 0.001 TYR A 644 PHE 0.019 0.001 PHE A1353 TRP 0.013 0.001 TRP A1030 HIS 0.004 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (14258) covalent geometry : angle 0.49743 / 0.26 (19397) SS BOND : bond 0.00080 / 0.04 ( 1) SS BOND : angle 0.42308 / 0.23 ( 2) hydrogen bonds : bond 0.03640 / 2.35 ( 447) hydrogen bonds : angle 4.72151 / 3.25 ( 1368) metal coordination : bond 0.01353 / 0.85 ( 16) metal coordination : angle 4.39822 / 2.77 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 825 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8546 (m-10) REVERT: A 874 MET cc_start: 0.9119 (mtm) cc_final: 0.8440 (mtp) REVERT: A 1436 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8387 (tm-30) REVERT: A 1458 ARG cc_start: 0.7754 (mmt180) cc_final: 0.6836 (mmm-85) REVERT: A 1507 MET cc_start: 0.8579 (mmm) cc_final: 0.8341 (mmm) outliers start: 11 outliers final: 6 residues processed: 41 average time/residue: 0.1198 time to fit residues: 7.8879 Evaluate side-chains 36 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1436 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 2 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.121331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.072302 restraints weight = 37871.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.073921 restraints weight = 19529.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.074849 restraints weight = 13897.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.075499 restraints weight = 11759.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.075860 restraints weight = 10714.619| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 14275 Z= 0.273 Angle : 0.605 10.962 19420 Z= 0.308 Chirality : 0.044 0.187 2080 Planarity : 0.004 0.049 2367 Dihedral : 11.904 173.723 2257 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.20 % Allowed : 15.07 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.21), residues: 1582 helix: 1.03 (0.25), residues: 441 sheet: -1.05 (0.30), residues: 275 loop : -1.21 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 467 TYR 0.011 0.001 TYR A 644 PHE 0.019 0.002 PHE A1353 TRP 0.016 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.27 (14258) covalent geometry : angle 0.58480 / 0.31 (19397) SS BOND : bond 0.00108 / 0.06 ( 1) SS BOND : angle 0.51159 / 0.28 ( 2) hydrogen bonds : bond 0.04411 / 2.80 ( 447) hydrogen bonds : angle 4.97063 / 3.41 ( 1368) metal coordination : bond 0.01795 / 0.93 ( 16) metal coordination : angle 4.80698 / 3.03 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 29 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 825 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8620 (m-10) REVERT: A 874 MET cc_start: 0.9085 (mtm) cc_final: 0.8392 (mtp) REVERT: A 1436 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: A 1458 ARG cc_start: 0.7823 (mmt180) cc_final: 0.6970 (mmm-85) REVERT: A 1507 MET cc_start: 0.8487 (mmm) cc_final: 0.8211 (mmm) outliers start: 17 outliers final: 8 residues processed: 43 average time/residue: 0.1087 time to fit residues: 7.6742 Evaluate side-chains 38 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1436 GLU Chi-restraints excluded: chain A residue 1564 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 25 optimal weight: 0.0870 chunk 77 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.123851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.074395 restraints weight = 37288.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.076231 restraints weight = 19216.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.077234 restraints weight = 13560.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.077920 restraints weight = 11388.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.078265 restraints weight = 10356.777| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14275 Z= 0.105 Angle : 0.481 9.226 19420 Z= 0.249 Chirality : 0.040 0.146 2080 Planarity : 0.003 0.048 2367 Dihedral : 11.648 173.463 2257 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.71 % Allowed : 15.36 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.21), residues: 1582 helix: 1.21 (0.25), residues: 449 sheet: -0.81 (0.31), residues: 272 loop : -1.04 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1053 TYR 0.010 0.001 TYR A 644 PHE 0.016 0.001 PHE A1353 TRP 0.012 0.001 TRP A1030 HIS 0.004 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (14258) covalent geometry : angle 0.46830 / 0.25 (19397) SS BOND : bond 0.00058 / 0.03 ( 1) SS BOND : angle 0.27796 / 0.15 ( 2) hydrogen bonds : bond 0.03113 / 2.03 ( 447) hydrogen bonds : angle 4.51628 / 3.12 ( 1368) metal coordination : bond 0.01220 / 0.88 ( 16) metal coordination : angle 3.41236 / 2.14 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 825 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8539 (m-10) REVERT: A 874 MET cc_start: 0.9060 (mtm) cc_final: 0.8425 (mtp) REVERT: A 1436 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8330 (tm-30) REVERT: A 1458 ARG cc_start: 0.7825 (mmt180) cc_final: 0.6953 (mmm-85) REVERT: A 1507 MET cc_start: 0.8518 (mmm) cc_final: 0.8225 (mmm) outliers start: 10 outliers final: 7 residues processed: 36 average time/residue: 0.0977 time to fit residues: 5.8580 Evaluate side-chains 36 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 951 CYS Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1436 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 94 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 100 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.121697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.072373 restraints weight = 37555.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.074051 restraints weight = 19684.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.075021 restraints weight = 14049.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.075615 restraints weight = 11850.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.075942 restraints weight = 10864.556| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 14275 Z= 0.242 Angle : 0.579 11.527 19420 Z= 0.293 Chirality : 0.043 0.172 2080 Planarity : 0.004 0.050 2367 Dihedral : 11.724 173.964 2257 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.42 % Allowed : 15.57 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.21), residues: 1582 helix: 1.28 (0.25), residues: 441 sheet: -0.83 (0.31), residues: 270 loop : -1.07 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 467 TYR 0.010 0.001 TYR A 644 PHE 0.018 0.001 PHE A1353 TRP 0.015 0.001 TRP A1030 HIS 0.004 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.24 (14258) covalent geometry : angle 0.56068 / 0.29 (19397) SS BOND : bond 0.00083 / 0.04 ( 1) SS BOND : angle 0.40646 / 0.22 ( 2) hydrogen bonds : bond 0.04093 / 2.60 ( 447) hydrogen bonds : angle 4.77173 / 3.28 ( 1368) metal coordination : bond 0.01531 / 0.81 ( 16) metal coordination : angle 4.40828 / 2.83 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 30 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.9197 (tpp) cc_final: 0.8939 (tpp) REVERT: A 223 ASP cc_start: 0.8455 (p0) cc_final: 0.7880 (t70) REVERT: A 417 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9349 (mt) REVERT: A 825 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8592 (m-10) REVERT: A 874 MET cc_start: 0.9125 (mtm) cc_final: 0.8463 (mtp) REVERT: A 1436 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8503 (tm-30) REVERT: A 1458 ARG cc_start: 0.7859 (mmt180) cc_final: 0.7070 (mmt180) outliers start: 20 outliers final: 14 residues processed: 47 average time/residue: 0.1176 time to fit residues: 8.6634 Evaluate side-chains 44 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 27 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 913 LYS Chi-restraints excluded: chain A residue 951 CYS Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1436 GLU Chi-restraints excluded: chain A residue 1564 THR Chi-restraints excluded: chain A residue 1596 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 121 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 34 optimal weight: 0.0270 chunk 146 optimal weight: 1.9990 chunk 149 optimal weight: 0.3980 chunk 103 optimal weight: 0.0570 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.124539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.075209 restraints weight = 37080.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.077131 restraints weight = 19021.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.078227 restraints weight = 13213.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.078751 restraints weight = 10993.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.079143 restraints weight = 10077.677| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14275 Z= 0.086 Angle : 0.470 8.133 19420 Z= 0.243 Chirality : 0.040 0.144 2080 Planarity : 0.003 0.050 2367 Dihedral : 11.513 173.658 2257 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.64 % Allowed : 16.07 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.21), residues: 1582 helix: 1.32 (0.25), residues: 456 sheet: -0.65 (0.31), residues: 278 loop : -0.98 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1053 TYR 0.010 0.001 TYR A 644 PHE 0.014 0.001 PHE A1353 TRP 0.010 0.001 TRP A1030 HIS 0.004 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 (14258) covalent geometry : angle 0.45895 / 0.24 (19397) SS BOND : bond 0.00036 / 0.02 ( 1) SS BOND : angle 0.20501 / 0.11 ( 2) hydrogen bonds : bond 0.02935 / 1.93 ( 447) hydrogen bonds : angle 4.39650 / 3.04 ( 1368) metal coordination : bond 0.01028 / 0.78 ( 16) metal coordination : angle 3.08816 / 1.96 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 524 TYR cc_start: 0.8622 (m-80) cc_final: 0.8413 (m-80) REVERT: A 583 MET cc_start: 0.8774 (mmm) cc_final: 0.8571 (mmm) REVERT: A 825 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8459 (m-10) REVERT: A 874 MET cc_start: 0.9046 (mtm) cc_final: 0.8420 (mtp) REVERT: A 1436 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8366 (tm-30) REVERT: A 1458 ARG cc_start: 0.8066 (mmt180) cc_final: 0.7229 (mmm-85) REVERT: A 1633 LYS cc_start: 0.8910 (mmmt) cc_final: 0.8705 (mmmt) outliers start: 9 outliers final: 5 residues processed: 36 average time/residue: 0.1036 time to fit residues: 6.0872 Evaluate side-chains 35 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1436 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 30.0000 chunk 159 optimal weight: 0.0270 chunk 19 optimal weight: 0.0010 chunk 65 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 148 optimal weight: 0.5980 chunk 126 optimal weight: 20.0000 overall best weight: 0.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1616 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.124677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.075098 restraints weight = 37233.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.077023 restraints weight = 19086.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.077973 restraints weight = 13465.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.078635 restraints weight = 11373.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.078980 restraints weight = 10378.989| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14275 Z= 0.087 Angle : 0.451 8.337 19420 Z= 0.232 Chirality : 0.039 0.142 2080 Planarity : 0.003 0.052 2367 Dihedral : 11.345 174.628 2257 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.78 % Allowed : 15.92 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.21), residues: 1582 helix: 1.52 (0.25), residues: 456 sheet: -0.54 (0.31), residues: 276 loop : -0.85 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 505 TYR 0.010 0.001 TYR A 644 PHE 0.013 0.001 PHE A1353 TRP 0.007 0.001 TRP A 607 HIS 0.004 0.000 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (14258) covalent geometry : angle 0.44035 / 0.23 (19397) SS BOND : bond 0.00024 / 0.01 ( 1) SS BOND : angle 0.15443 / 0.08 ( 2) hydrogen bonds : bond 0.02746 / 1.79 ( 447) hydrogen bonds : angle 4.26643 / 2.94 ( 1368) metal coordination : bond 0.01045 / 0.77 ( 16) metal coordination : angle 3.02601 / 1.95 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 825 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8544 (m-10) REVERT: A 874 MET cc_start: 0.9016 (mtm) cc_final: 0.8421 (mtp) REVERT: A 1458 ARG cc_start: 0.8049 (mmt180) cc_final: 0.7164 (mmm-85) outliers start: 11 outliers final: 6 residues processed: 41 average time/residue: 0.1230 time to fit residues: 7.8242 Evaluate side-chains 35 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1436 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 109 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 148 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.124120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.074741 restraints weight = 37369.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.076524 restraints weight = 19115.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.077547 restraints weight = 13483.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.078187 restraints weight = 11323.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.078311 restraints weight = 10325.189| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14275 Z= 0.118 Angle : 0.479 8.124 19420 Z= 0.246 Chirality : 0.040 0.142 2080 Planarity : 0.004 0.052 2367 Dihedral : 11.318 174.444 2257 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.64 % Allowed : 16.21 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.21), residues: 1582 helix: 1.56 (0.25), residues: 456 sheet: -0.46 (0.31), residues: 271 loop : -0.86 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 467 TYR 0.009 0.001 TYR A 644 PHE 0.020 0.001 PHE A 376 TRP 0.008 0.001 TRP A1030 HIS 0.004 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (14258) covalent geometry : angle 0.46815 / 0.25 (19397) SS BOND : bond 0.00026 / 0.01 ( 1) SS BOND : angle 0.17598 / 0.09 ( 2) hydrogen bonds : bond 0.03028 / 1.96 ( 447) hydrogen bonds : angle 4.29568 / 2.96 ( 1368) metal coordination : bond 0.01083 / 0.73 ( 16) metal coordination : angle 3.09999 / 2.01 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 223 ASP cc_start: 0.8423 (p0) cc_final: 0.7681 (t70) REVERT: A 825 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8564 (m-10) REVERT: A 874 MET cc_start: 0.9066 (mtm) cc_final: 0.8434 (mtp) REVERT: A 1436 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8379 (tm-30) REVERT: A 1458 ARG cc_start: 0.8109 (mmt180) cc_final: 0.7252 (mmm-85) outliers start: 9 outliers final: 5 residues processed: 39 average time/residue: 0.1194 time to fit residues: 7.2559 Evaluate side-chains 36 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1436 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 80 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 126 optimal weight: 0.4980 chunk 17 optimal weight: 0.0060 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 157 optimal weight: 9.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.124740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.075537 restraints weight = 37266.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.077296 restraints weight = 19007.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.078417 restraints weight = 13327.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.078935 restraints weight = 11131.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.079305 restraints weight = 10211.349| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14275 Z= 0.094 Angle : 0.464 7.501 19420 Z= 0.237 Chirality : 0.039 0.140 2080 Planarity : 0.003 0.052 2367 Dihedral : 11.259 174.456 2257 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.57 % Allowed : 16.21 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.21), residues: 1582 helix: 1.61 (0.25), residues: 455 sheet: -0.43 (0.31), residues: 271 loop : -0.83 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1053 TYR 0.009 0.001 TYR A 644 PHE 0.013 0.001 PHE A1353 TRP 0.010 0.001 TRP A1030 HIS 0.004 0.000 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 (14258) covalent geometry : angle 0.45414 / 0.24 (19397) SS BOND : bond 0.00008 / 0.00 ( 1) SS BOND : angle 0.13688 / 0.07 ( 2) hydrogen bonds : bond 0.02791 / 1.82 ( 447) hydrogen bonds : angle 4.24255 / 2.93 ( 1368) metal coordination : bond 0.01036 / 0.75 ( 16) metal coordination : angle 2.90594 / 1.87 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2645.85 seconds wall clock time: 46 minutes 18.84 seconds (2778.84 seconds total)